Wilkerson, M.D., Ru, Y., and Brendel, V.P. (2009) Common introns within orthologous genes: software and application to plants Briefings in Bioinformatics, 10(6), 631-644. [abstract] [PDF]
PlantGDB News:Community-annotated maize gene models (see an example at ZmGDB) are now displayed at both MaizeGDB and maizesequence.org, by means of Distributed Annotation Service (DAS) (November 21, 2009).
Brachypodium distachyon browser: BdGDB, a genome browser for the model grass species Brachypodium distachyon, is now available, based on the JGI v1.0 8x genome assembly. The assembly displayed comprises 271.15 Mb arranged in 5 pseudochromosomes. Display includes gene models, splice-aligned EST, cDNA, PUT assembly and Arabidopsis and rice predicted proteins (October 30, 2009).
Currently, I am mostly concerned with graduate education, although I taught undergraduate courses prior to coming to ISU and I have undergraduate research students in my group. I have also been on the faculty of the 2010 ISU Computational and Systems Biology Summer Institute and prior ISU summer institutes. My basic approach to teaching in an academic setting is to emphasize the integration of research and textbook learning. This connection is quite obvious in my Bioinformatics II. Advanced Genome Informatics course, as much of the material derives from recent research papers. In my classroom and one-on-one teaching I seek to encourage the students to learn by asking interesting questions and then pursuing logical ways to derive answers for themselves. Even when dealing with classical textbook material, I strongly believe that such approach is essential for a student to "own" the material for him- or herself.
A second point of emphasis in my teaching is interdisciplinary study. Bioinformatics and computational biology require knowledge of molecular biology, statistics, and computer science, and I require students to attain the necessary background in all these disciplines, independent of their initial biases towards any one field. I seek to encourage the students to go beyond their current limitations, although I am only successful in this with the very best and most highly motivated students. In my class, I typically organize the students in groups of four with combined expertise in the different areas. The groups are assigned different tasks throughout the term. This arrangement has proved very successful in getting the students to interact across the different study programs and seems an excellent way of introducing them to interdisciplinary work environments they will encounter later in their academic or business careers.
My teaching style strongly favors self-motivated and resourceful students. For example, a core part of my Bioinformatics and Computational Biology course is a final project specific to each student (or group) and initiated by him or her (or the group). I explain to the students that the final projects are entirely for their own benefit, a chance to review and deepen their study of a particular topic covered in the class. Students typically prepare a short talk to the class and produce a written account of their work in research paper format. I believe this approach has worked very well as judged by the quality of the submitted work and students' comments. I pursue a similar approach with rotation students by assigning them a small project in their interest area but leaving it up to their initiative to find creative ways to tackle the project. In my experience so far, this has separated students quite sharply into those that eagerly engage and others that essentially end up doing nothing. I expect a level of maturity in a graduate student to make his or her own choices in that respect. Although adhering to these teaching principles, I seek to engage with the students sufficiently to perceive individual strengths and personality differences and try to make appropriate adjustments for the individual student.